I would see them more as more random PRG type characters in rural/random maps (omg big guy with a 50 cal sniper rifle on a hill surrounded by aliens, lets save him), not national guard people in a city... though I guess that really doesn't fit the Xenonauts vibe now that I think about it. Hmmm. It would add some color/variation to the missions though. It might be better down the road as a DLC pack or something.
I do agree that the general npc troops should be clearly inferior.